title: Identification of microRNA-Like RNAs in the filamentous fungus Trichoderma reesei by solexa sequencing.
abstract: microRNAs (miRNAs) are non-coding small RNAs (sRNAs) capable of negatively regulating gene expression. Recently, microRNA-like small RNAs (milRNAs) were discovered in several filamentous fungi but not yet in Trichoderma reesei, an industrial filamentous fungus that can secrete abundant hydrolases. To explore the presence of milRNA in T. reesei and evaluate their expression under induction of cellulose, two T. reesei sRNA libraries of cellulose induction (IN) and non-induction (CON) were generated and sequenced using Solexa sequencing technology. A total of 726 and 631 sRNAs were obtained from the IN and CON samples, respectively. Global expression analysis showed an extensively differential expression of sRNAs in T. reesei under the two conditions. Thirteen predicted milRNAs were identified in T. reesei based on the short hairpin structure analysis. The milRNA profiles obtained in deep sequencing were further validated by RT-qPCR assay. Computational analysis predicted a number of potential targets relating to many processes including regulation of enzyme expression. The presence and differential expression of T. reesei milRNAs imply that milRNA might play a role in T. reesei growth and cellulase induction. This work lays foundation for further functional study of fungal milRNAs and their industrial application.
authors.affiliation: College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China ; College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Kang
authors.initials: K
authors.lastname: Kang
authors.forename: Jiasheng
authors.initials: J
authors.lastname: Zhong
authors.forename: Liang
authors.initials: L
authors.lastname: Jiang
authors.forename: Gang
authors.initials: G
authors.lastname: Liu
authors.forename: Christine Yuan
authors.initials: CY
authors.lastname: Gou
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wu
authors.forename: You
authors.initials: Y
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Luo
authors.forename: Deming
authors.initials: D
authors.lastname: Gou
mesh_terms: D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D009690:Nucleic Acid Conformation; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics*; D014242:Trichoderma / Q000235:genetics* / Q000254:growth & development
chemical_list: D035683:MicroRNAs; D012331:RNA, Fungal